2012 Annual Report 1a.Objectives (from AD-416): The discovery of genes or quantitative trait loci (QTL) that control yield per se in elite soybean germplasm. 1b.Approach (from AD-416): The high yield reference genotype, IA3023, was crossed to 25 diverse accessions to create 25 populations with 200 recombinant inbred lines (RILs) each. Thus, each population shares the reference genotype as one of the parents. The 5000 RILs will be phenotyped by collaborators and genotyped with SNPs as per a typical QTL population analysis. The 25 diverse accessions will be extensively genotyped or sequenced which allows for high marker density which can be extrapolated to all the RILs in the 25 populations, thus greatly increasing the power to detect and fine map QTL. Using this approach, essentially all SNPs present in all 5000 RILs can be determined and the most common QTL among the 25 diverse lines can be discovered. 3.Progress Report: Funds are provided by the United Soybean Board, as part of Project #9241 entitled “Nested Association Mapping to Identify Yield QTL in Diverse High Yielding Elite Soybean Lines”. This project is being undertaken for the purpose of identifying genetic factors that positively impact soybean yield. Soybean progeny are being developed from matings of the high yielding soybean variety IA3023 with a broad spectrum of soybean lines from soybean breeders in Arkansas, Illinois, Indiana, Ohio, Tennessee, Missouri, and Nebraska. A total of 5,600 recombinant inbred soybean lines were developed from 40 crosses with IA3023. These lines are now being tested in replicated yield trials with the goal of applying Nested Association Mapping to discover genes that underlie soybean productivity. Progress was made in the discovery of single nucleotide polymorphism DNA markers that will be used in the molecular genetic analysis of the 5,600 recombinant inbred lines and parents. DNA sequence data were obtained from the 41 Nested Association Mapping parents using the “next generation” Illumina HiSeq DNA sequencer at the USDA, Beltsville. The sequence of each of the parents was aligned to the Williams 82 Whole Genome Sequence (Glyma1.0). Following alignment and further analysis of the sequence data, a total of 118,958 high quality SNPs were discovered. These SNPs are now being further analyzed to select a final set of 6,000 SNPs that will be included on an Illumina iSelect beadchip that will be used to analyze the 5,600 recombinant inbred lines and parents.